How to avoid vertex sorting after using Offset Polygons in Animation Nodes?
The Offset Polygons node doesn't just transform the vertices/polygons of the mesh, it also splits polygons if they are connected. So it is impossible to retain the order of vertices in most of the cases, and in cases where it is possible, it is not worth it to consider it as a special case.

So if you want to retain the order of vertices, manually loop over the polygon indices, transform the vertices and write them to their respective locations in the vertices list. Let me know if you want more details on how to do that.